|
| Status |
Public on Jan 06, 2023 |
| Title |
Post_challenge vYF D259 CO314_D259 |
| Sample type |
SRA |
| |
|
| Source name |
Whole Blood
|
| Organism |
Macaca fascicularis |
| Characteristics |
tissue: Whole Blood
Sex: male
treatment: vYF
time: 259
|
| Treatment protocol |
36 male NHPs were randomized into groups of nine to receive subcutaneous injection in the deltoid muscle region of the upper arm with a single commercial dose of Stamaril (4 LogCCID50) or YF-VAX (6 LogCCID50), or 4 or 5 LogCCID50 vYF at WSL stage. Nine months after vaccination, NHPs along with six additional unvaccinated controls were challenged by a single sub-cutaneous injection of 3.0 LogCCID50 wild-type YFV Asibi strain in the scapula region.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Whole blood from NHPs was collected in PAXgene tubes (BD762165 –Ozyme) and stored according to the manufacturer's protocol. Total RNA was extracted with the PAXgene 96 Blood RNA kit (Qiagen-762331) according to manufacturer’s instructions on Tecan Evo150 workstation
Extracted RNA samples were processed using the GLOBINclear™-Human kit (ThermoFisher - AM1980) for the depletion of the alpha and beta globin mRNA according to manufacturer’s instructions. Sequencing libraries were prepared with the TruSeq mRNA stranded kit (Illumina - 20162122/20146602) using 300 ng of total globin-depleted RNA according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Post_challenge vYF D259
post challenge (vaccinated animals)
|
| Data processing |
OmicSoft Array Studio software (v9.0 -v10.0).
The reads were aligned with OmicsSoft Aligner (OSA4) in Array Studio against the Cyno.WashU2013 reference genome using WashUGene20140620 gene annotations
Naïve read count quantification was performed with the Array Studio software using WashUGene20140620 gene annotations
Multiple mappings reads and first-read-forward-strand reads were discarded from the analysis
Read counts were then subsequently analyzed using R scripts (R version 3.3.3).
All samples were scale-normalized according to their library size by the TMM method of edgeR package (v3.16.5) and transformed with voom (Limma R package v3.30.13).
For the linear modeling of differential gene expression, a model was built with Limma using the treatment condition (vaccination group and sampling time point) as a factor (relatively to the vaccination day defined as a baseline). Contrasts were set up in order to compare for every vaccination group each time point post-vaccination with baseline (Day –29)). Contrasts were also set up to compare directly vaccination groups for each time point post-vaccination relatively to their own group baseline
The tmod R package (v0.31) was used to detect functional enrichment directly on the Limma object (i.e. inference test result from the Limma R package) on the full genes list (ordered using default "minimal significant difference" ranking) coming from each contrast
Assembly: Cyno.WashU2013
Supplementary files format and content: Raw read counts from Array Studio software
|
| |
|
| Submission date |
Jan 05, 2023 |
| Last update date |
Jan 06, 2023 |
| Contact name |
Emilie Chautard |
| E-mail(s) |
emilie.chautard@sanofi.com
|
| Organization name |
Sanofi
|
| Street address |
1541 Avenue Marcel Mérieux
|
| City |
Marcy L'Etoile |
| ZIP/Postal code |
69280 |
| Country |
France |
| |
|
| Platform ID |
GPL22523 |
| Series (1) |
| GSE222229 |
Evaluation of safety and immuno-efficacy of a next generation live attenuated yellow fever vaccine in cynomolgus macaques |
|
| Relations |
| BioSample |
SAMN32600895 |
| SRA |
SRX18944297 |
